samtools mpileup include soft-clipped bases

Question

[noodle]

Hi biostars,

Is someone aware of a convenient way to include soft-clipped bases with 'samtools mpileup'?

[rfran010]

is there more context to this question or a reason you think they are not included by default?

[noodle]

Just want to compare how many bases I lose from clipping with different parameters

[rfran010]

Hard to see how it's possible since soft-clipped bases technically don't have an aligned position... Maybe it would make sense to just input alignments from your different parameter runs to get the side-by-side coverage, e.g.

samtools pileup reads.param1.bam reads.param2.bam

and then you could do some custom summary if needed.

[noodle]

Ya, I just settled on doing 'endtoend' alignments instead of 'local' so the bases aren't clipped

[Pierre Lindenbaum]

don't you mean

is it possible to include the soft-clipped BASES in "samtools mpileup" ?